Little is known about the effects of center-pivot irrigation on soil aggregation as well as soil organic (SOC) and inorganic (SIC) carbon stocks in semi-arid agro-ecosystems, in particular at deeper depths. This study was conducted to determine if cropland under irrigation can sequester additional carbon as SOC or SIC and improve soil aggregation compared to rainfed cropland.  Sampling sites were selected in two climatic regions of the Central Great Plains: an area near Imperial, Nebraska and a more arid area near Otis, Colorado. At both locations, three different treatments were selected: a non-cultivated native grassland (NG), a center-pivot irrigated (CP) and an adjacent dryland (DL) cultivated system. Soil samples were taken at 0-5, 5-20, 20-50 and 50-75 cm depths and analyzed for SOC and SIC. Aggregate size distribution was determined in the surface 0-5 and 5-20 cm layers. Significantly greater SOC stocks were found in the 0-20 cm soil layers of CP compared to DL systems at both locations. In the entire 0-75 cm, SOC stocks were also greater under CP than DL, but this was only statistically significant at Imperial. Irrigation also resulted in greater macroaggregate (> 250 mm) levels in the 0-5 cm depth at both locations, especially in the more arid, no-tilled sites at Otis. Soil inorganic C stocks were significantly higher in cultivated (CP and DL) compared to grassland soils, but did not differ between CP and DL. In the sampled 0-75 cm depth, SIC accounted for nearly 50% of the total soil C storage in the cultivated systems at Imperial and 30% at Otis.  High accumulations of SIC in these cultivated semi-arid lands are most likely due to cultivation-induced changes in soil properties, water regime and carbonate-forming ion concentrations.